DOCSLIB.ORG

Mutations of the Transcriptional Corepressor ZMYM2 Cause Syndromic Urinary Tract Malformations

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Mutations of the Transcriptional Corepressor ZMYM2 Cause Syndromic Urinary Tract Malformations ARTICLE Mutations of the Transcriptional Corepressor ZMYM2 Cause Syndromic Urinary Tract Malformations Dervla M. Connaughton,1,2,46 Rufeng Dai,1,3,46 Danielle J. Owen,4 Jonathan Marquez,5 Nina Mann,1 Adda L. Graham-Paquin,6 Makiko Nakayama,1 Etienne Coyaud,7,8 Estelle M.N. Laurent,7,8 Jonathan R. St-Germain,7 Lot Snijders Blok,9,10,11 Arianna Vino,9 Verena Kla¨mbt,1 Konstantin Deutsch,1 Chen-Han Wilfred Wu,1 Caroline M. Kolvenbach,1 Franziska Kause,1 Isabel Ottlewski,1 Ronen Schneider,1 Thomas M. Kitzler,1 Amar J. Majmundar,1 Florian Buerger,1 Ana C. Onuchic-Whitford,1,12 Mao Youying,1 Amy Kolb,1 Daanya Salmanullah,1 Evan Chen,1 Amelie T. van der Ven,1 Jia Rao,3 Hadas Ityel,1 Steve Seltzsam,1 Johanna M. Rieke,1 Jing Chen,1 Asaf Vivante,1,13 Daw-Yang Hwang,1 Stefan Kohl,1 Gabriel C. Dworschak,1 (Author list continued on next page) Summary Congenital anomalies of the kidney and urinary tract (CAKUT) constitute one of the most frequent birth defects and represent the most common cause of chronic kidney disease in the first three decades of life. Despite the discovery of dozens of monogenic causes of CA- KUT, most pathogenic pathways remain elusive. We performed whole-exome sequencing (WES) in 551 individuals with CAKUT and identified a heterozygous de novo stop-gain variant in ZMYM2 in two different families with CAKUT. Through collaboration, we identi- fied in total 14 different heterozygous loss-of-function mutations in ZMYM2 in 15 unrelated families. Most mutations occurred de novo, indicating possible interference with reproductive function. Human disease features are replicated in X. tropicalis larvae with morpho- lino knockdowns, in which expression of truncated ZMYM2 proteins, based on individual mutations, failed to rescue renal and cranio- facial defects. Moreover, heterozygous Zmym2-deficient mice recapitulated features of CAKUT with high penetrance. The ZMYM2 protein is a component of a transcriptional corepressor complex recently linked to the silencing of developmentally regulated endoge- nous retrovirus elements. Using protein-protein interaction assays, we show that ZMYM2 interacts with additional epigenetic silencing complexes, as well as confirming that it binds to FOXP1, a transcription factor that has also been linked to CAKUT. In summary, our findings establish that loss-of-function mutations of ZMYM2, and potentially that of other proteins in its interactome, as causes of hu- man CAKUT, offering new routes for studying the pathogenesis of the disorder. Introduction genes thus far implicated in monogenic forms of CAKUT account for only 14%–20% of cases.3–5 Thus, a significant Congenital anomalies of the kidney and urinary tract (CA- proportion of CAKUT is still molecularly unidentified and KUT) constitute one of the most frequent birth defects, many pathogenic pathways are still elusive.2 To gain causing almost 50% of all cases of end-stage kidney disease further insight into the pathogenesis of human CAKUT, (ESKD) in the first three decades of life.1 In humans, the we performed whole-exome sequencing (WES) in a large identification of 40 monogenic causes of isolated CAKUT international cohort of 551 individuals from different fam- and 153 monogenic causes of syndromic CAKUT has al- ilies with CAKUT. We identified 14 different heterozygous lowed delineation of multiple pathways of human CAKUT mutations in ZMYM2 in 15 unrelated families (19 affected including those involving bone morphogenic protein individuals) with syndromic CAKUT who also had extrare- signaling and retinoic acid signaling.2,3 However, the nal features. ZMYM2 (MIM: 602221), previously known as 1Department of Pediatrics, Boston Children’s Hospital, Harvard Medical School, Boston, MA 02115, USA; 2Division of Nephrology, Department of Medi- cine, University Hospital - London Health Sciences Centre, Schulich School of Medicine & Dentistry, Western University, 339 Windermere Road, London, ON N6A 5A5, Canada; 3Department of Nephrology, Children’s Hospital of Fudan University, 201102 Shanghai, China; 4Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9PT, UK; 5Pediatric Genomics Discovery Program, Department of Pediatrics and Genetics, Yale Univer- sity School of Medicine, New Haven, CT 06520, USA; 6Rosalind & Morris Goodman Cancer Research Centre and Department of Biochemistry, McGill Uni- versity, Montre´al, QC H3A 1A3, Canada; 7Princess Margaret Cancer Centre, University Health Network & Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 1L7, Canada; 8Univ. Lille, Inserm, CHU Lille, U1192 - Prote´omique Re´ponse Inflammatoire Spectrome´trie de Masse - PRISM, 59000 Lille, France; 9Language and Genetics Department, Max Planck Institute for Psycholinguistics, 6525 XD Nijmegen, the Netherlands; 10Donders Insti- tute for Brain, Cognition and Behaviour, Radboud University, 6500HE Nijmegen, the Netherlands; 11Human Genetics Department, Radboud University Medical Center, 6500HB Nijmegen, the Netherlands; 12Renal Division, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA; 13Tel Aviv University, Faculty of Medicine, Tel Aviv-Yafo 6997801, Israel; 14Amsterdam UMC, University of Amsterdam, Department of Clinical (Affiliations continued on next page) Ó 2020 American Society of Human Genetics. The American Journal of Human Genetics 107, 727–742, October 1, 2020 727 Tobias Hermle,1 Marie¨lle Alders,14 Tobias Bartolomaeus,15 Stuart B. Bauer,16 Michelle A. Baum,1 Eva H. Brilstra,17 Thomas D. Challman,18 Jacob Zyskind,19 Carrie E. Costin,20 Katrina M. Dipple,21 Floor A. Duijkers,22 Marcia Ferguson,23 David R. Fitzpatrick,24 Roger Fick,25 Ian A. Glass,21 Peter J. Hulick,26 Antonie D. Kline,23 Ilona Krey,15,27 Selvin Kumar,28 Weining Lu,29 Elysa J. Marco,30 Ingrid M. Wentzensen,19 Heather C. Mefford,21 Konrad Platzer,15 Inna S. Povolotskaya,31 Juliann M. Savatt,18 Natalia V. Shcherbakova,31 Prabha Senguttuvan,32 Audrey E. Squire,33 Deborah R. Stein,1 Isabelle Thiffault,34,35,36 Victoria Y. Voinova,31 Michael J.G. Somers,1 Michael A. Ferguson,1 Avram Z. Traum,1 Ghaleb H. Daouk,1 Ankana Daga,1 Nancy M. Rodig,1 Paulien A. Terhal,17 Ellen van Binsbergen,17 Loai A. Eid,37 Velibor Tasic,38 Hila Milo Rasouly,39 Tze Y. Lim,39 Dina F. Ahram,39 Ali G. Gharavi,39 Heiko M. Reutter,40,41 Heidi L. Rehm,42,43 Daniel G. MacArthur,42,43 Monkol Lek,42,43 Kristen M. Laricchia,42,43 Richard P. Lifton,44 Hong Xu,3 Shrikant M. Mane,45 Simone Sanna-Cherchi,39 Andrew D. Sharrocks,4 Brian Raught,7 Simon E. Fisher,9,10 Maxime Bouchard,6 Mustafa K. Khokha,5 Shirlee Shril,1 and Friedhelm Hildebrandt1,* FIM, ZNF198, or RAMP, is a nuclear zinc finger protein that clinical data, pedigree data, and blood samples from individuals localizes to the nucleus, specifically to the PML body.6 It with CAKUT from worldwide sources using a standardized ques- forms part of a transcriptional complex acting as a core- tionnaire. Informed consent was obtained from the individuals pressor by interacting with different nuclear receptors, and/or the substitute decision maker, as appropriate. The diag- and the LSD1-CoREST-HDAC1 complex on chromatin.7 nosis of CAKUT was made by nephrologists and/or urologists based on relevant imaging. The role of ZMYM2 in kidney and ureter development is Whole-exome sequencing was performed as previously largely unknown and ZMYM2 mutations have not previ- 3 described. Briefly, DNA samples from affected individuals and ously been implicated in kidney disease. unaffected family members were subjected to WES using Agilent SureSelect human exome capture arrays (Life Technologies) with next generation sequencing (NGS) on an Illumina sequencing Material and Methods platform. Sequence reads were mapped against the human reference genome (NCBI build 37/hg19) using CLC Genomics Subjects, Whole-Exome Sequencing, and Variant Workbench (v.6.5.1) software (CLC bio). Mutation analysis was Evaluation performed under recessive, dominant, or de novo models, as pre- Approval for human subjects research was obtained from the Insti- viously published.3,8,9 Mutation analysis was performed by genet- tutional Review Boards of the University of Michigan, Boston icists and cell biologists, who had knowledge regarding clinical Children’s Hospital, and from other relevant local Ethics Review phenotypes, pedigree structure, and genetic mapping, and was Boards. The procedures followed in this study were in accordance in line with proposed guidelines.10,11 Sequence variants remain- with the ethical standards of the responsible committee on hu- ing after WES evaluation were examined for segregation. Filtering man experimentation. Proper informed consent was obtained was performed to retain only alleles with a minor allele frequency from all participants. Following informed consent, we obtained (MAF) < 0.1%, a widely accepted cutoff for autosomal-dominant Genetics, Meibergdreef 9, 1105 Amsterdam, Netherlands; 15Institute of Human Genetics, University of Leipzig Medical Center, Philipp-Rosenthal- Straße 55, 04103 Leipzig, Germany; 16Department of Urology, Boston Children’s Hospital, Harvard Medical School, Boston, MA 02115, USA; 17Department of Genetics, University Medical Center Utrecht, Heidelberglaan 100, 3584 CX Utrecht, the Netherlands; 18Geisinger, Autism & Developmental Medicine Insti- tute, 100 N Academy Avenue, Danville, PA 17822, USA; 19Department of Clinical Genomics, GeneDx, 207 Perry Pkwy, Gaithersburg, MD 20877, USA; 20Department of Clinical Genetics, Akron Children’s Hospital, One Perkins Square, Akron, OH 44308, USA; 21Division
Load more

Recommended publications
  • 1 Supporting Information for a Microrna Network Regulates
    Supporting Information for A microRNA Network Regulates Expression and Biosynthesis of CFTR and CFTR-ΔF508 Shyam Ramachandrana,b, Philip H. Karpc, Peng Jiangc, Lynda S. Ostedgaardc, Amy E. Walza, John T. Fishere, Shaf Keshavjeeh, Kim A. Lennoxi, Ashley M. Jacobii, Scott D. Rosei, Mark A. Behlkei, Michael J. Welshb,c,d,g, Yi Xingb,c,f, Paul B. McCray Jr.a,b,c Author Affiliations: Department of Pediatricsa, Interdisciplinary Program in Geneticsb, Departments of Internal Medicinec, Molecular Physiology and Biophysicsd, Anatomy and Cell Biologye, Biomedical Engineeringf, Howard Hughes Medical Instituteg, Carver College of Medicine, University of Iowa, Iowa City, IA-52242 Division of Thoracic Surgeryh, Toronto General Hospital, University Health Network, University of Toronto, Toronto, Canada-M5G 2C4 Integrated DNA Technologiesi, Coralville, IA-52241 To whom correspondence should be addressed: Email: [email protected] (M.J.W.); yi- [email protected] (Y.X.); Email: [email protected] (P.B.M.) This PDF file includes: Materials and Methods References Fig. S1. miR-138 regulates SIN3A in a dose-dependent and site-specific manner. Fig. S2. miR-138 regulates endogenous SIN3A protein expression. Fig. S3. miR-138 regulates endogenous CFTR protein expression in Calu-3 cells. Fig. S4. miR-138 regulates endogenous CFTR protein expression in primary human airway epithelia. Fig. S5. miR-138 regulates CFTR expression in HeLa cells. Fig. S6. miR-138 regulates CFTR expression in HEK293T cells. Fig. S7. HeLa cells exhibit CFTR channel activity. Fig. S8. miR-138 improves CFTR processing. Fig. S9. miR-138 improves CFTR-ΔF508 processing. Fig. S10. SIN3A inhibition yields partial rescue of Cl- transport in CF epithelia.
    [Show full text]
  • Screen for Multi-SUMO–Binding Proteins Reveals a Multi-SIM–Binding Mechanism for Recruitment of the Transcriptional Regulator ZMYM2 to Chromatin
    Screen for multi-SUMO–binding proteins reveals a multi-SIM–binding mechanism for recruitment of the transcriptional regulator ZMYM2 to chromatin Elisa Aguilar-Martineza, Xi Chena, Aaron Webbera, A. Paul Moulda, Anne Seifertb, Ronald T. Hayb, and Andrew D. Sharrocksa,1 aFaculty of Life Sciences, University of Manchester, Manchester M13 9PT, United Kingdom; and bCentre for Gene Regulation and Expression, University of Dundee, Dundee DD1 5EH, United Kingdom Edited by James L. Manley, Columbia University, New York, NY, and approved July 17, 2015 (received for review May 20, 2015) Protein SUMOylation has emerged as an important regulatory human proteins containing two or more motifs corresponding event, particularly in nuclear processes such as transcriptional to the extended negatively charged amino acid-dependent control and DNA repair. In this context, small ubiquitin-like modifier SUMOylation motif (NDSM) (13) Thus, there is a huge poten- (SUMO) often provides a binding platform for the recruitment of tial for widespread multi-SUMOylation of proteins to occur. proteins via their SUMO-interacting motifs (SIMs). Recent discoveries Indeed, several of these proteins have been shown to be point to an important role for multivalent SUMO binding through SUMOylated on multiple sites, including megakaryoblastic leu- multiple SIMs in the binding partner as exemplified by poly- kemia (translocation) 1 (MKL1) (14), CREB-binding protein SUMOylation acting as a binding platform for ubiquitin E3 ligases (CBP) (15), and PEA3/ETV4 (16). Furthermore, two recent such as ring finger protein 4. Here, we have investigated whether proteomic studies emphasize the potential for more widespread other types of protein are recruited through multivalent SUMO multi-SUMOylation as they found that a large proportion of all interactions.
    [Show full text]
  • T-Cell Lymphoblastic Lymphoma Arising in the Setting of Myeloid/Lymphoid Neoplasms with Eosinophilia
    cancers Article T-Cell Lymphoblastic Lymphoma Arising in the Setting of Myeloid/Lymphoid Neoplasms with Eosinophilia: LMO2 Immunohistochemistry as a Potentially Useful Diagnostic Marker Magda Zanelli 1 , Giuseppe G. Loscocco 2,3 , Elena Sabattini 4, Maurizio Zizzo 5,6,* , Francesca Sanguedolce 7, Luigi Panico 8, Daniela Fanni 9, Raffaella Santi 10, Cecilia Caprera 11, Cristiana Rossi 12, Alessandra Soriano 13,14, Alberto Cavazza 1, Alessandro Giunta 5, Cristina Mecucci 15, Alessandro M. Vannucchi 2,3, Stefano A. Pileri 16 and Stefano Ascani 11,15 1 Pathology Unit, Azienda Unità Sanitaria Locale—IRCCS di Reggio Emilia, 42123 Reggio Emilia, Italy; [email protected] (M.Z.); [email protected] (A.C.) 2 Department of Experimental and Clinical Medicine, University of Florence, 50134 Florence, Italy; gloscocco@unifi.it (G.G.L.); a.vannucchi@unifi.it (A.M.V.) 3 Center of Research and Innovation of Myeloproliferative Neoplasms (CRIMM), Azienda Ospedaliero-Universitaria Careggi, 50139 Florence, Italy 4 Citation: Zanelli, M.; Loscocco, G.G.; Haematopathology Unit, IRCCS Azienda Ospedaliero-Universitaria di Bologna, 40138 Bologna, Italy; Sabattini, E.; Zizzo, M.; [email protected] 5 Sanguedolce, F.; Panico, L.; Fanni, D.; Surgical Oncology Unit, Azienda Unità Sanitaria Locale—IRCCS di Reggio Emilia, 42123 Reggio Emilia, Italy; [email protected] Santi, R.; Caprera, C.; Rossi, C.; et al. 6 Clinical and Experimental Medicine PhD Program, University of Modena and Reggio Emilia, T-Cell Lymphoblastic Lymphoma 41121 Modena, Italy Arising in the Setting of 7 Pathology Unit, Azienda Ospedaliero-Universitaria—Ospedali Riuniti di Foggia, 71122 Foggia, Italy; Myeloid/Lymphoid Neoplasms with [email protected] Eosinophilia: LMO2 8 Pathology Unit Azienda Ospedaliera dei Colli Monaldi-Cotugno-CTO, P.O.
    [Show full text]
  • Characterizing Genomic Duplication in Autism Spectrum Disorder by Edward James Higginbotham a Thesis Submitted in Conformity
    Characterizing Genomic Duplication in Autism Spectrum Disorder by Edward James Higginbotham A thesis submitted in conformity with the requirements for the degree of Master of Science Graduate Department of Molecular Genetics University of Toronto © Copyright by Edward James Higginbotham 2020 i Abstract Characterizing Genomic Duplication in Autism Spectrum Disorder Edward James Higginbotham Master of Science Graduate Department of Molecular Genetics University of Toronto 2020 Duplication, the gain of additional copies of genomic material relative to its ancestral diploid state is yet to achieve full appreciation for its role in human traits and disease. Challenges include accurately genotyping, annotating, and characterizing the properties of duplications, and resolving duplication mechanisms. Whole genome sequencing, in principle, should enable accurate detection of duplications in a single experiment. This thesis makes use of the technology to catalogue disease relevant duplications in the genomes of 2,739 individuals with Autism Spectrum Disorder (ASD) who enrolled in the Autism Speaks MSSNG Project. Fine-mapping the breakpoint junctions of 259 ASD-relevant duplications identified 34 (13.1%) variants with complex genomic structures as well as tandem (193/259, 74.5%) and NAHR- mediated (6/259, 2.3%) duplications. As whole genome sequencing-based studies expand in scale and reach, a continued focus on generating high-quality, standardized duplication data will be prerequisite to addressing their associated biological mechanisms. ii Acknowledgements I thank Dr. Stephen Scherer for his leadership par excellence, his generosity, and for giving me a chance. I am grateful for his investment and the opportunities afforded me, from which I have learned and benefited. I would next thank Drs.
    [Show full text]
  • Identification of Disease Gene Variants That Can Lead to Familial Myelodysplasia and Acute Myeloid Leukaemia
    Identification of disease gene variants that can lead to familial myelodysplasia and acute myeloid leukaemia A thesis submitted for the degree of PhD Shirleny Romualdo Cardoso Supervisors: Professor Inderjeet Dokal, and Professor Tom Vulliamy Centre for Genomics and Child Health, Blizard Institute Barts and The London School of Medicine & Dentistry, Queen Mary University of London In loving memory of my beloved sister Karla Romualdo Cardoso 2 I, Shirleny Romualdo Cardoso, confirm that the research included within this thesis is my own work or that where it has been carried out in collaboration with, or supported by others, that this is duly acknowledged below and my contribution indicated. Previously published material is also acknowledged below. I attest that I have exercised reasonable care to ensure that the work is original, and does not to the best of my knowledge break any UK law, infringe any third party’s copyright or other Intellectual Property Right, or contain any confidential material. I accept that the College has the right to use plagiarism detection software to check the electronic version of the thesis. I confirm that this thesis has not been previously submitted for the award of a degree by this or any other university. The copyright of this thesis rests with the author and no quotation from it or information derived from it may be published without the prior written consent of the author. Shirleny Romualdo Cardoso 3 Abstract Myelodysplasia (MDS) is characterised by inefficient haematopoiesis with dysplastic features of blood and bone marrow, reduction of mature blood cells and continuous bone marrow failure (BMF).
    [Show full text]
  • Cancer Drug Resistance
    Cowell et al. Cancer Drug Resist 2021;4:607-19 Cancer DOI: 10.20517/cdr.2021.30 Drug Resistance Review Open Access Mechanisms of resistance to FGFR1 inhibitors in FGFR1-driven leukemias and lymphomas: implications for optimized treatment John K. Cowell, Tianxiang Hu Georgia Cancer Center, 1410 Laney Walker Blvd, Augusta, GA 30912, USA. Correspondence to: Prof. John K. Cowell, CN2133, Georgia Cancer Center, 1410 Laney Walker Blvd, Augusta, GA 30912, USA. E- mail: [email protected] How to cite this article: Cowell JK, Hu T. Mechanisms of resistance to FGFR1 inhibitors in FGFR1-driven leukemias and lymphomas: implications for optimized treatment. Cancer Drug Resist 2021;4:607-19. https://dx.doi.org/10.20517/cdr.2021.30 Received: 6 Apr 2021 First Decision: 28 Apr 2021 Revised: 14 May 2021 Accepted: 24 May 2021 First online: 25 May 2021 Academic Editor: Godefridus J. Peters Copy Editor: Yue-Yue Zhang Production Editor: Yue-Yue Zhang Abstract Myeloid and lymphoid neoplasms with eosinophilia and FGFR1 rearrangements (MLN-eo FGFR1) disease is derived from a pluripotent hematopoietic stem cell and has a complex presentation with a myeloproliferative disorder with or without eosinophilia and frequently presents with mixed lineage T- or B-lymphomas. The myeloproliferative disease frequently progresses to AML and lymphoid neoplasms can develop into acute lymphomas. No matter the cell type involved, or clinical presentation, chromosome translocations involving the FGFR1 kinase and various partner genes, which leads to constitutive activation of downstream oncogenic signaling cascades. These patients are not responsive to treatment regimens developed for other acute leukemias and survival is poor.
    [Show full text]
  • ZBTB33 Is Mutated in Clonal Hematopoiesis and Myelodysplastic Syndromes and Impacts RNA Splicing
    RESEARCH ARTICLE ZBTB33 Is Mutated in Clonal Hematopoiesis and Myelodysplastic Syndromes and Impacts RNA Splicing Ellen M. Beauchamp1,2, Matthew Leventhal1,2, Elsa Bernard3, Emma R. Hoppe4,5,6, Gabriele Todisco7,8, Maria Creignou8, Anna Gallì7, Cecilia A. Castellano1,2, Marie McConkey1,2, Akansha Tarun1,2, Waihay Wong1,2, Monica Schenone2, Caroline Stanclift2, Benjamin Tanenbaum2, Edyta Malolepsza2, Björn Nilsson1,2,9, Alexander G. Bick2,10,11, Joshua S. Weinstock12, Mendy Miller2, Abhishek Niroula1,2, Andrew Dunford2, Amaro Taylor-Weiner2, Timothy Wood2, Alex Barbera2, Shankara Anand2; Bruce M. Psaty13,14, Pinkal Desai15, Michael H. Cho16,17, Andrew D. Johnson18, Ruth Loos19,20; for the NHLBI Trans-Omics for Precision Medicine (TOPMed) Consortium; Daniel G. MacArthur2,21,22,23, Monkol Lek2,21,24; for the Exome Aggregation Consortium, Donna S. Neuberg25, Kasper Lage2,26, Steven A. Carr2, Eva Hellstrom-Lindberg8, Luca Malcovati7, Elli Papaemmanuil3, Chip Stewart2, Gad Getz2,27,28, Robert K. Bradley4,5,6, Siddhartha Jaiswal29, and Benjamin L. Ebert1,2,30 Downloaded from https://bloodcancerdiscov.aacrjournals.org by guest on September 30, 2021. Copyright 2021 American Copyright 2021 by AssociationAmerican for Association Cancer Research. for Cancer Research. ABSTRACT Clonal hematopoiesis results from somatic mutations in cancer driver genes in hematopoietic stem cells. We sought to identify novel drivers of clonal expansion using an unbiased analysis of sequencing data from 84,683 persons and identified common mutations in the 5-methylcytosine reader ZBTB33 as well as in YLPM1, SRCAP, and ZNF318. We also identified these mutations at low frequency in patients with myelodysplastic syndrome. Zbtb33-edited mouse hematopoietic stem and progenitor cells exhibited a competitive advantage in vivo and increased genome-wide intron retention.
    [Show full text]
  • A Global Transcriptional Network Connecting Noncoding Mutations to Changes in Tumor Gene Expression
    ARTICLES https://doi.org/10.1038/s41588-018-0091-2 A global transcriptional network connecting noncoding mutations to changes in tumor gene expression Wei Zhang 1,8*, Ana Bojorquez-Gomez1,8, Daniel Ortiz Velez2, Guorong Xu3, Kyle S. Sanchez1, John Paul Shen 1, Kevin Chen2, Katherine Licon1, Collin Melton4, Katrina M. Olson1,5, Michael Ku Yu1, Justin K. Huang1,6, Hannah Carter 1, Emma K. Farley1,5, Michael Snyder4, Stephanie I. Fraley2, Jason F. Kreisberg1* and Trey Ideker 1,2,6,7* Although cancer genomes are replete with noncoding mutations, the effects of these mutations remain poorly characterized. Here we perform an integrative analysis of 930 tumor whole genomes and matched transcriptomes, identifying a network of 193 noncoding loci in which mutations disrupt target gene expression. These ‘somatic eQTLs’ (expression quantitative trait loci) are frequently mutated in specific cancer tissues, and the majority can be validated in an independent cohort of 3,382 tumors. Among these, we find that the effects of noncoding mutations on DAAM1, MTG2 and HYI transcription are recapitu- lated in multiple cancer cell lines and that increasing DAAM1 expression leads to invasive cell migration. Collectively, the non- coding loci converge on a set of core pathways, permitting a classification of tumors into pathway-based subtypes. The somatic eQTL network is disrupted in 88% of tumors, suggesting widespread impact of noncoding mutations in cancer. uman cancers are fundamentally heterogeneous, with many Results distinct subtypes associated with differences
    [Show full text]
  • Content Based Search in Gene Expression Databases and a Meta-Analysis of Host Responses to Infection
    Content Based Search in Gene Expression Databases and a Meta-analysis of Host Responses to Infection A Thesis Submitted to the Faculty of Drexel University by Francis X. Bell in partial fulfillment of the requirements for the degree of Doctor of Philosophy November 2015 c Copyright 2015 Francis X. Bell. All Rights Reserved. ii Acknowledgments I would like to acknowledge and thank my advisor, Dr. Ahmet Sacan. Without his advice, support, and patience I would not have been able to accomplish all that I have. I would also like to thank my committee members and the Biomed Faculty that have guided me. I would like to give a special thanks for the members of the bioinformatics lab, in particular the members of the Sacan lab: Rehman Qureshi, Daisy Heng Yang, April Chunyu Zhao, and Yiqian Zhou. Thank you for creating a pleasant and friendly environment in the lab. I give the members of my family my sincerest gratitude for all that they have done for me. I cannot begin to repay my parents for their sacrifices. I am eternally grateful for everything they have done. The support of my sisters and their encouragement gave me the strength to persevere to the end. iii Table of Contents LIST OF TABLES.......................................................................... vii LIST OF FIGURES ........................................................................ xiv ABSTRACT ................................................................................ xvii 1. A BRIEF INTRODUCTION TO GENE EXPRESSION............................. 1 1.1 Central Dogma of Molecular Biology........................................... 1 1.1.1 Basic Transfers .......................................................... 1 1.1.2 Uncommon Transfers ................................................... 3 1.2 Gene Expression ................................................................. 4 1.2.1 Estimating Gene Expression ............................................ 4 1.2.2 DNA Microarrays ......................................................
    [Show full text]
  • 8P11 Myeloproliferative Syndrome
    8p11 myeloproliferative syndrome Description 8p11 myeloproliferative syndrome is a blood cancer that involves different types of blood cells. Blood cells are divided into several groups (lineages) based on the type of early cell from which they are descended. Two of these lineages are myeloid cells and lymphoid cells. Individuals with 8p11 myeloproliferative syndrome can develop both myeloid cell cancer and lymphoid cell cancer. The condition can occur at any age. It usually begins as a myeloproliferative disorder, which is characterized by a high number of white blood cells (leukocytes). Most affected individuals also have an excess of myeloid cells known as eosinophils (eosinophilia). In addition to a myeloproliferative disorder, many people with 8p11 myeloproliferative syndrome develop lymphoma, which is a form of blood cancer that involves lymphoid cells. The cancerous lymphoid cells grow and divide in lymph nodes, forming a tumor that enlarges the lymph nodes. In most cases of 8p11 myeloproliferative syndrome, the cancerous cells are lymphoid cells called T cells. Lymphoma can develop at the same time as the myeloproliferative disorder or later. In most people with 8p11 myeloproliferative syndrome, the myeloproliferative disorder develops into a fast-growing blood cancer called acute myeloid leukemia. The rapid myeloid and lymphoid cell production caused by these cancers results in enlargement of the spleen and liver (splenomegaly and hepatomegaly, respectively). Most people with 8p11 myeloproliferative syndrome have symptoms such as fatigue or night sweats. Some affected individuals have no symptoms, and the condition is discovered through routine blood tests. Frequency The prevalence of 8p11 myeloproliferative syndrome is unknown. It is thought to be a rare condition.
    [Show full text]
  • Coexpression Networks Based on Natural Variation in Human Gene Expression at Baseline and Under Stress
    University of Pennsylvania ScholarlyCommons Publicly Accessible Penn Dissertations Fall 2010 Coexpression Networks Based on Natural Variation in Human Gene Expression at Baseline and Under Stress Renuka Nayak University of Pennsylvania, [email protected] Follow this and additional works at: https://repository.upenn.edu/edissertations Part of the Computational Biology Commons, and the Genomics Commons Recommended Citation Nayak, Renuka, "Coexpression Networks Based on Natural Variation in Human Gene Expression at Baseline and Under Stress" (2010). Publicly Accessible Penn Dissertations. 1559. https://repository.upenn.edu/edissertations/1559 This paper is posted at ScholarlyCommons. https://repository.upenn.edu/edissertations/1559 For more information, please contact [email protected]. Coexpression Networks Based on Natural Variation in Human Gene Expression at Baseline and Under Stress Abstract Genes interact in networks to orchestrate cellular processes. Here, we used coexpression networks based on natural variation in gene expression to study the functions and interactions of human genes. We asked how these networks change in response to stress. First, we studied human coexpression networks at baseline. We constructed networks by identifying correlations in expression levels of 8.9 million gene pairs in immortalized B cells from 295 individuals comprising three independent samples. The resulting networks allowed us to infer interactions between biological processes. We used the network to predict the functions of poorly-characterized human genes, and provided some experimental support. Examining genes implicated in disease, we found that IFIH1, a diabetes susceptibility gene, interacts with YES1, which affects glucose transport. Genes predisposing to the same diseases are clustered non-randomly in the network, suggesting that the network may be used to identify candidate genes that influence disease susceptibility.
    [Show full text]
  • Table S1. 103 Ferroptosis-Related Genes Retrieved from the Genecards
    Table S1. 103 ferroptosis-related genes retrieved from the GeneCards. Gene Symbol Description Category GPX4 Glutathione Peroxidase 4 Protein Coding AIFM2 Apoptosis Inducing Factor Mitochondria Associated 2 Protein Coding TP53 Tumor Protein P53 Protein Coding ACSL4 Acyl-CoA Synthetase Long Chain Family Member 4 Protein Coding SLC7A11 Solute Carrier Family 7 Member 11 Protein Coding VDAC2 Voltage Dependent Anion Channel 2 Protein Coding VDAC3 Voltage Dependent Anion Channel 3 Protein Coding ATG5 Autophagy Related 5 Protein Coding ATG7 Autophagy Related 7 Protein Coding NCOA4 Nuclear Receptor Coactivator 4 Protein Coding HMOX1 Heme Oxygenase 1 Protein Coding SLC3A2 Solute Carrier Family 3 Member 2 Protein Coding ALOX15 Arachidonate 15-Lipoxygenase Protein Coding BECN1 Beclin 1 Protein Coding PRKAA1 Protein Kinase AMP-Activated Catalytic Subunit Alpha 1 Protein Coding SAT1 Spermidine/Spermine N1-Acetyltransferase 1 Protein Coding NF2 Neurofibromin 2 Protein Coding YAP1 Yes1 Associated Transcriptional Regulator Protein Coding FTH1 Ferritin Heavy Chain 1 Protein Coding TF Transferrin Protein Coding TFRC Transferrin Receptor Protein Coding FTL Ferritin Light Chain Protein Coding CYBB Cytochrome B-245 Beta Chain Protein Coding GSS Glutathione Synthetase Protein Coding CP Ceruloplasmin Protein Coding PRNP Prion Protein Protein Coding SLC11A2 Solute Carrier Family 11 Member 2 Protein Coding SLC40A1 Solute Carrier Family 40 Member 1 Protein Coding STEAP3 STEAP3 Metalloreductase Protein Coding ACSL1 Acyl-CoA Synthetase Long Chain Family Member 1 Protein
    [Show full text]